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Annotated SLURM

This is a walk-through for a basic SLURM scheduler job script for a common case of a multi-threaded analysis. If the program you run is single-threaded (can use only one CPU core) then only use '--ntasks=1' line for the cpu request instead of all three listed lines. Annotations are marked with bullet points.

The full script is provided at the end of the article. Values in brackets (<>) are placeholders. You need to replace them with your own values (e.g. change <JOBNAME> to something like "blast_proj22"). We will write additional documentation on more complex job layouts for MPI jobs and other situations when a simple number of processor cores is not sufficient.

Set the shell to use

#!/bin/bash

Common SBATCH options

job-name

job-name is used to name the job to make it easier to see in the job queue.

#SBATCH --job-name=<JOBNAME>

mail-user and mail-type

mail-user allows users to provie an email address to use for batch system communications.

#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-user=<EMAIL-ONE>,<EMAIL-TWO>

mail-type allows users to filter when emails should be sent to the provided addresses by providing one or more (comma-separated) of the following options:

  • NONE - No emails for this job.
  • ALL - All emails for this job.
  • BEGIN - Email when this job starts.
  • END - Email a summary at the end of the job.
  • FAIL - Email if this job fails.
#SBATCH --mail-type=FAIL,END

output and error

output and error are paths to where the stdout and stderr for the script should be written to after a job runs.

Some common file patterns:

  • %j - Job ID
  • %A-%a - Array job ID (A) and task ID (a)
#SBATCH --output <my_job_%j.out>

nodes

nodes indicates the number of nodes to use when running this script. For all non-MPI jobs, this number will be equal to 1.

#SBATCH --nodes=1

ntasks

ntasks indicates the number of tasks associated with this script. For all non-MPI jobs, this number will be equal to 1.

#SBATCH --ntasks=1

cpus-per-task

cpus-per-task indicates the number of CPU cores to use when running this script. This number must match the argument used for the program being run.

#SBATCH --cpus-per-task=4

mem

mem indicates the total memory limit for the job. Units can be specified with mb (megabytes) or gb (gigabytes). The default memory is 2 gigabytes.

#SBATCH --mem=4gb

time

time indicates the job's total run time. The run time is formatted days:hours:minutes:seconds. days is optional, but should be used when convenient. The default run time is 10 minutes.

#SBATCH --time=72:00:00

account

account indicates what group this script belongs to.

#SBATCH --account=<GROUP>

array

array will create a job array for the script, which creates many jobs (called array tasks) that differ only in their $SLURM_ARRAY_TASK_ID.

#SBATCH --array=<BEGIN-END>

#SBATCH --array=<1-5>

Host/time/directory information

It is recommended to add host, time, and directory information to your job script using hostname, date, and pwd.

hostname;date;pwd

It is also recommended to add an extra call of date to the end of a script.

module load

To ensure your script can run correctly, use module load to load the environment modules necessary to access the software needed for the script.

module load ncbi_blast

Full shell script example

#SBATCH --job-name=<JOBNAME>
#SBATCH --mail-user=<ACCOUNT>@ufl.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --output=/blue/<ACCOUNT>/job-outs/blastn.out
#SBATCH --err=/blue/<ACCOUNT>/job-outs/blastn.err
#SBATCH --cpus-per-task=4
#SBATCH --mem=8gb
#SBATCH --time=2:00:00

hostname;pwd;date

module load ncbi_blast

blastn -db nt -query input.fa -outfmt 6 -out results.xml --num_threads 4
date